Birds have a reputation of having rather simple brains. Sure, they can react to stimuli to avoid danger and survive, e.g. if I kick a chicken it will probably try to avoid me, but is this just automatic instinct or is there something deeper? Does something happen in the bird's mind along the lines of "boy that kick was unpleasant, I sure wish it hadn't happened and I hope it doesn't happen again"? Do birds experience negative emotions?

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Yes. This article from 2005 summarises the scientific knowledge on birds feeling pain.

It's worth taking a moment to define pain, as there is often confusion about this. The definition of pain from the International Association for the Study of Pain is:

An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.

That is, pain implies actual suffering. On the other hand, 'automatic instinct' in which an organism reacts to negative stimuli but does not necessarily feel any associated emotions is called nociception. Even single-celled organisms can display nociception.

The position of the article is that yes, birds feel pain, there's plenty of evidence indicating such (the article has 40 references), it's clear that they mean pain in the sense defined above, and they go on to describe how said pain should be treated. Here are some notable quotes:

It is generally accepted that birds perceive pain similarly to mammals. Birds have neurologic components to respond to painful stimuli

it is advisable to treat for pain when dealing with any condition expected to cause pain, especially if known to be painful in humans

Although it is unclear at this time at what taxonomic level nociception is associated with pain and whether all species, including humans, feel pain with the same qualities and intensities, operationally, vertebrates and some invertebrates feel pain.

Unquestionably, the experience of pain must be aversive and unpleasant to motivate a bird or any other animal to change its behavior. In plain language, pain hurts regardless of the species.

Pain is an individual sensory and emotional experience

just because an animal (or a bird in the case of this review) may have a different pain experience from that of humans does not mean that the animal's pain does not exist.

More details can be found in the 'Evaluating Pain and Pain-Associated Behavior' section.

It goes beyond pain though. A recent study found that hens feel empathy for their chicks:

When chicks were exposed to puffs of air, they showed signs of distress that were mirrored by their mothers. The hens' heart rate increased, their eye temperature lowered - a recognised stress sign - and they became increasingly alert. Levels of preening were reduced, and the hens made more clucking noises directed at their chicks.

We found that adult female birds possess at least one of the essential underpinning attributes of 'empathy', the ability to be affected by, and share, the emotional state of another.